Multiple sequence alignment - TraesCS4B01G299800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4B01G299800 chr4B 100.000 2587 0 0 1 2587 586332528 586329942 0.000000e+00 4778.0
1 TraesCS4B01G299800 chr4B 87.695 577 54 9 1802 2365 671846134 671846706 0.000000e+00 656.0
2 TraesCS4B01G299800 chr4B 92.857 42 2 1 317 357 243018280 243018239 2.780000e-05 60.2
3 TraesCS4B01G299800 chr4B 92.857 42 2 1 317 357 343256119 343256078 2.780000e-05 60.2
4 TraesCS4B01G299800 chr4D 92.483 1051 53 15 590 1616 467999213 467998165 0.000000e+00 1480.0
5 TraesCS4B01G299800 chr4D 95.812 597 23 1 1 597 467999828 467999234 0.000000e+00 963.0
6 TraesCS4B01G299800 chr4D 86.082 582 62 10 1802 2365 105132891 105133471 2.200000e-170 608.0
7 TraesCS4B01G299800 chr4D 94.444 36 1 1 323 357 300747314 300747279 1.000000e-03 54.7
8 TraesCS4B01G299800 chr4A 90.503 1074 57 22 592 1638 3219800 3220855 0.000000e+00 1376.0
9 TraesCS4B01G299800 chr4A 87.583 604 59 10 1 597 3219181 3219775 0.000000e+00 686.0
10 TraesCS4B01G299800 chr4A 84.694 588 66 11 1801 2365 535233922 535233336 1.340000e-157 566.0
11 TraesCS4B01G299800 chr4A 82.036 167 9 8 1660 1805 3245177 3245343 3.500000e-24 122.0
12 TraesCS4B01G299800 chr4A 92.857 42 2 1 317 357 585815837 585815796 2.780000e-05 60.2
13 TraesCS4B01G299800 chr3D 89.062 576 45 12 1801 2365 5645984 5645416 0.000000e+00 699.0
14 TraesCS4B01G299800 chr1D 88.596 570 52 11 1804 2365 494861799 494862363 0.000000e+00 680.0
15 TraesCS4B01G299800 chr1D 88.042 577 56 6 1802 2365 78119159 78118583 0.000000e+00 671.0
16 TraesCS4B01G299800 chr1D 97.561 41 1 0 315 355 476766202 476766162 1.280000e-08 71.3
17 TraesCS4B01G299800 chr1D 92.857 42 2 1 317 357 127885798 127885839 2.780000e-05 60.2
18 TraesCS4B01G299800 chr3B 87.241 580 56 10 1802 2364 602245005 602244427 0.000000e+00 645.0
19 TraesCS4B01G299800 chr3B 85.110 591 59 14 1804 2365 123036473 123035883 6.210000e-161 577.0
20 TraesCS4B01G299800 chr3B 98.261 230 4 0 2358 2587 609445322 609445093 1.110000e-108 403.0
21 TraesCS4B01G299800 chr3B 98.678 227 3 0 2361 2587 763460869 763461095 1.110000e-108 403.0
22 TraesCS4B01G299800 chr3B 98.261 230 3 1 2359 2587 241302957 241303186 4.010000e-108 401.0
23 TraesCS4B01G299800 chr3B 92.776 263 14 4 2326 2587 399686474 399686732 2.430000e-100 375.0
24 TraesCS4B01G299800 chr3B 100.000 29 0 0 287 315 672500325 672500297 1.000000e-03 54.7
25 TraesCS4B01G299800 chr1B 87.031 586 58 8 1798 2365 26266717 26267302 0.000000e+00 645.0
26 TraesCS4B01G299800 chr2A 87.002 577 62 6 1801 2365 38396096 38396671 2.810000e-179 638.0
27 TraesCS4B01G299800 chr2A 95.885 243 9 1 2346 2587 166862319 166862561 2.410000e-105 392.0
28 TraesCS4B01G299800 chr2A 98.413 63 1 0 2303 2365 581383817 581383755 7.570000e-21 111.0
29 TraesCS4B01G299800 chr5D 86.213 602 56 9 1801 2375 45684375 45683774 6.080000e-176 627.0
30 TraesCS4B01G299800 chr2D 86.348 586 64 9 1794 2365 364970215 364969632 2.190000e-175 625.0
31 TraesCS4B01G299800 chr2D 100.000 31 0 0 285 315 628933100 628933070 1.000000e-04 58.4
32 TraesCS4B01G299800 chr6A 82.609 598 64 16 1804 2365 613150978 613150385 2.310000e-135 492.0
33 TraesCS4B01G299800 chr6B 98.678 227 2 1 2362 2587 529725511 529725285 4.010000e-108 401.0
34 TraesCS4B01G299800 chr5B 95.528 246 8 3 2343 2587 461832919 461833162 8.680000e-105 390.0
35 TraesCS4B01G299800 chr5B 92.857 42 2 1 317 357 163339768 163339809 2.780000e-05 60.2
36 TraesCS4B01G299800 chr3A 98.206 223 4 0 2365 2587 714907560 714907338 8.680000e-105 390.0
37 TraesCS4B01G299800 chr3A 100.000 31 0 0 285 315 23192156 23192126 1.000000e-04 58.4
38 TraesCS4B01G299800 chr7B 98.198 222 4 0 2366 2587 585038248 585038027 3.120000e-104 388.0
39 TraesCS4B01G299800 chr7B 93.182 44 2 1 315 357 347173405 347173362 2.150000e-06 63.9
40 TraesCS4B01G299800 chr7A 84.337 83 10 2 277 356 654193275 654193357 7.680000e-11 78.7
41 TraesCS4B01G299800 chr2B 97.727 44 1 0 312 355 647110975 647111018 2.760000e-10 76.8
42 TraesCS4B01G299800 chr7D 90.476 42 3 1 317 357 312091236 312091277 1.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G299800 chr4B 586329942 586332528 2586 True 4778.0 4778 100.0000 1 2587 1 chr4B.!!$R3 2586
1 TraesCS4B01G299800 chr4B 671846134 671846706 572 False 656.0 656 87.6950 1802 2365 1 chr4B.!!$F1 563
2 TraesCS4B01G299800 chr4D 467998165 467999828 1663 True 1221.5 1480 94.1475 1 1616 2 chr4D.!!$R2 1615
3 TraesCS4B01G299800 chr4D 105132891 105133471 580 False 608.0 608 86.0820 1802 2365 1 chr4D.!!$F1 563
4 TraesCS4B01G299800 chr4A 3219181 3220855 1674 False 1031.0 1376 89.0430 1 1638 2 chr4A.!!$F2 1637
5 TraesCS4B01G299800 chr4A 535233336 535233922 586 True 566.0 566 84.6940 1801 2365 1 chr4A.!!$R1 564
6 TraesCS4B01G299800 chr3D 5645416 5645984 568 True 699.0 699 89.0620 1801 2365 1 chr3D.!!$R1 564
7 TraesCS4B01G299800 chr1D 494861799 494862363 564 False 680.0 680 88.5960 1804 2365 1 chr1D.!!$F2 561
8 TraesCS4B01G299800 chr1D 78118583 78119159 576 True 671.0 671 88.0420 1802 2365 1 chr1D.!!$R1 563
9 TraesCS4B01G299800 chr3B 602244427 602245005 578 True 645.0 645 87.2410 1802 2364 1 chr3B.!!$R2 562
10 TraesCS4B01G299800 chr3B 123035883 123036473 590 True 577.0 577 85.1100 1804 2365 1 chr3B.!!$R1 561
11 TraesCS4B01G299800 chr1B 26266717 26267302 585 False 645.0 645 87.0310 1798 2365 1 chr1B.!!$F1 567
12 TraesCS4B01G299800 chr2A 38396096 38396671 575 False 638.0 638 87.0020 1801 2365 1 chr2A.!!$F1 564
13 TraesCS4B01G299800 chr5D 45683774 45684375 601 True 627.0 627 86.2130 1801 2375 1 chr5D.!!$R1 574
14 TraesCS4B01G299800 chr2D 364969632 364970215 583 True 625.0 625 86.3480 1794 2365 1 chr2D.!!$R1 571
15 TraesCS4B01G299800 chr6A 613150385 613150978 593 True 492.0 492 82.6090 1804 2365 1 chr6A.!!$R1 561

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
940 998 0.027586 CTTGCCATTAACGCCTACGC 59.972 55.0 0.0 0.0 45.53 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1796 1871 0.036875 GTGGAGTTGGCCTAAGCTGT 59.963 55.0 3.32 0.0 39.73 4.4 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 0.113190 ACTGGCAAGGGAGGGAAAAG 59.887 55.000 0.00 0.00 0.00 2.27
185 186 5.066634 CAGCGACTTACTTTCTGAGGATAGA 59.933 44.000 0.00 0.00 0.00 1.98
243 244 9.832445 AACACTAGTTGAAAAGTGATTCTAGAA 57.168 29.630 7.82 7.82 44.79 2.10
366 370 2.433604 AGAGGGAGTATCATGCACACAG 59.566 50.000 0.00 0.00 36.25 3.66
530 537 4.438744 GCAGATACCGGTGAGAATTTTTGG 60.439 45.833 19.93 0.00 0.00 3.28
550 557 3.772025 TGGGGAAAAAGAAACTTCAGCAA 59.228 39.130 0.00 0.00 0.00 3.91
755 797 3.371168 GGGCGAATATTGTACGTACGAA 58.629 45.455 24.41 14.71 0.00 3.85
759 801 5.220191 GGCGAATATTGTACGTACGAACAAA 60.220 40.000 24.41 8.66 38.95 2.83
883 933 2.812358 TCAACAAGTCGCTAGCTCAA 57.188 45.000 13.93 0.00 0.00 3.02
888 938 1.989165 CAAGTCGCTAGCTCAACTCAC 59.011 52.381 13.93 0.00 0.00 3.51
893 943 1.406069 CGCTAGCTCAACTCACCCATT 60.406 52.381 13.93 0.00 0.00 3.16
915 967 0.801872 TCCATTGCCATTCACGTTCG 59.198 50.000 0.00 0.00 0.00 3.95
920 972 0.317160 TGCCATTCACGTTCGTCTCT 59.683 50.000 0.00 0.00 0.00 3.10
921 973 0.992802 GCCATTCACGTTCGTCTCTC 59.007 55.000 0.00 0.00 0.00 3.20
924 976 2.663602 CCATTCACGTTCGTCTCTCTTG 59.336 50.000 0.00 0.00 0.00 3.02
925 977 1.767289 TTCACGTTCGTCTCTCTTGC 58.233 50.000 0.00 0.00 0.00 4.01
933 991 2.876091 TCGTCTCTCTTGCCATTAACG 58.124 47.619 0.00 0.00 0.00 3.18
940 998 0.027586 CTTGCCATTAACGCCTACGC 59.972 55.000 0.00 0.00 45.53 4.42
989 1052 8.997621 ACTACGAGCATCTCTAAAATTTGTTA 57.002 30.769 0.00 0.00 0.00 2.41
1041 1104 2.363795 TTCCAGATCGGCGAGGGT 60.364 61.111 17.22 0.00 33.14 4.34
1132 1201 0.034059 GATCATACAGCCCTCACCGG 59.966 60.000 0.00 0.00 0.00 5.28
1310 1379 3.948470 CGTCTTCGTGTACAAGTAAGC 57.052 47.619 8.68 6.89 0.00 3.09
1311 1380 3.562505 CGTCTTCGTGTACAAGTAAGCT 58.437 45.455 8.68 0.00 0.00 3.74
1318 1387 5.877031 TCGTGTACAAGTAAGCTAGATCAC 58.123 41.667 8.68 0.00 0.00 3.06
1319 1388 5.646793 TCGTGTACAAGTAAGCTAGATCACT 59.353 40.000 8.68 0.00 0.00 3.41
1345 1416 6.327365 TGCACCTTCCTCATTCAATCTCTATA 59.673 38.462 0.00 0.00 0.00 1.31
1348 1419 9.083422 CACCTTCCTCATTCAATCTCTATACTA 57.917 37.037 0.00 0.00 0.00 1.82
1390 1461 3.055385 TGAGATTCTTACGGTTCTTGGGG 60.055 47.826 0.00 0.00 0.00 4.96
1394 1465 4.703379 TTCTTACGGTTCTTGGGGTTAA 57.297 40.909 0.00 0.00 0.00 2.01
1426 1497 3.052082 GCAAGCCTTCTGCAGCGA 61.052 61.111 9.47 0.00 44.83 4.93
1448 1519 1.218047 GTGCCGGTGTCAGCAGATA 59.782 57.895 1.90 0.00 40.28 1.98
1499 1570 2.357034 GTCAGGAAGCGCCGTGAA 60.357 61.111 2.29 0.00 43.43 3.18
1617 1692 3.515502 AGATCCTTGCTGTACTTGCAGTA 59.484 43.478 12.37 5.17 41.71 2.74
1621 1696 1.808411 TGCTGTACTTGCAGTAAGCC 58.192 50.000 9.44 0.00 44.83 4.35
1627 1702 2.867109 ACTTGCAGTAAGCCAGTGAT 57.133 45.000 0.00 0.00 46.45 3.06
1632 1707 4.286297 TGCAGTAAGCCAGTGATAAACT 57.714 40.909 0.00 0.00 44.83 2.66
1638 1713 7.275920 CAGTAAGCCAGTGATAAACTAAGGAT 58.724 38.462 0.00 0.00 36.83 3.24
1639 1714 7.225538 CAGTAAGCCAGTGATAAACTAAGGATG 59.774 40.741 0.00 0.00 36.83 3.51
1640 1715 5.957771 AGCCAGTGATAAACTAAGGATGA 57.042 39.130 0.00 0.00 36.83 2.92
1641 1716 6.506538 AGCCAGTGATAAACTAAGGATGAT 57.493 37.500 0.00 0.00 36.83 2.45
1642 1717 6.904626 AGCCAGTGATAAACTAAGGATGATT 58.095 36.000 0.00 0.00 36.83 2.57
1643 1718 7.349598 AGCCAGTGATAAACTAAGGATGATTT 58.650 34.615 0.00 0.00 36.83 2.17
1644 1719 7.836183 AGCCAGTGATAAACTAAGGATGATTTT 59.164 33.333 0.00 0.00 36.83 1.82
1645 1720 8.470002 GCCAGTGATAAACTAAGGATGATTTTT 58.530 33.333 0.00 0.00 36.83 1.94
1685 1760 9.753674 AAGGATGATTAGTTAGGACAAATTTCA 57.246 29.630 0.00 0.00 0.00 2.69
1686 1761 9.753674 AGGATGATTAGTTAGGACAAATTTCAA 57.246 29.630 0.00 0.00 0.00 2.69
1708 1783 9.841295 TTCAAGTCCTAAATTTGTAGTACAACT 57.159 29.630 15.31 7.63 37.90 3.16
1709 1784 9.268268 TCAAGTCCTAAATTTGTAGTACAACTG 57.732 33.333 15.31 4.54 37.90 3.16
1710 1785 9.052759 CAAGTCCTAAATTTGTAGTACAACTGT 57.947 33.333 15.31 8.14 37.90 3.55
1725 1800 4.134563 ACAACTGTACAAGTAGGCTTTGG 58.865 43.478 0.00 0.00 38.56 3.28
1726 1801 3.418684 ACTGTACAAGTAGGCTTTGGG 57.581 47.619 0.00 0.00 37.36 4.12
1727 1802 2.709397 ACTGTACAAGTAGGCTTTGGGT 59.291 45.455 0.00 0.00 37.36 4.51
1728 1803 3.137728 ACTGTACAAGTAGGCTTTGGGTT 59.862 43.478 0.00 0.00 37.36 4.11
1729 1804 3.482436 TGTACAAGTAGGCTTTGGGTTG 58.518 45.455 0.00 0.00 31.49 3.77
1730 1805 2.748209 ACAAGTAGGCTTTGGGTTGT 57.252 45.000 0.00 0.00 31.49 3.32
1731 1806 3.026707 ACAAGTAGGCTTTGGGTTGTT 57.973 42.857 0.00 0.00 31.49 2.83
1732 1807 4.173290 ACAAGTAGGCTTTGGGTTGTTA 57.827 40.909 0.00 0.00 31.49 2.41
1733 1808 4.538738 ACAAGTAGGCTTTGGGTTGTTAA 58.461 39.130 0.00 0.00 31.49 2.01
1734 1809 4.583073 ACAAGTAGGCTTTGGGTTGTTAAG 59.417 41.667 0.00 0.00 31.49 1.85
1735 1810 4.717279 AGTAGGCTTTGGGTTGTTAAGA 57.283 40.909 0.00 0.00 0.00 2.10
1736 1811 5.056553 AGTAGGCTTTGGGTTGTTAAGAA 57.943 39.130 0.00 0.00 0.00 2.52
1737 1812 5.451354 AGTAGGCTTTGGGTTGTTAAGAAA 58.549 37.500 0.00 0.00 0.00 2.52
1738 1813 4.937201 AGGCTTTGGGTTGTTAAGAAAG 57.063 40.909 0.00 0.00 0.00 2.62
1739 1814 3.641436 AGGCTTTGGGTTGTTAAGAAAGG 59.359 43.478 0.00 0.00 0.00 3.11
1740 1815 3.639561 GGCTTTGGGTTGTTAAGAAAGGA 59.360 43.478 0.00 0.00 0.00 3.36
1741 1816 4.283467 GGCTTTGGGTTGTTAAGAAAGGAT 59.717 41.667 0.00 0.00 0.00 3.24
1742 1817 5.221641 GGCTTTGGGTTGTTAAGAAAGGATT 60.222 40.000 0.00 0.00 0.00 3.01
1743 1818 5.926542 GCTTTGGGTTGTTAAGAAAGGATTC 59.073 40.000 0.00 0.00 35.70 2.52
1744 1819 6.462347 GCTTTGGGTTGTTAAGAAAGGATTCA 60.462 38.462 0.00 0.00 38.06 2.57
1745 1820 7.425224 TTTGGGTTGTTAAGAAAGGATTCAA 57.575 32.000 0.00 0.00 38.06 2.69
1746 1821 7.425224 TTGGGTTGTTAAGAAAGGATTCAAA 57.575 32.000 0.00 0.00 38.06 2.69
1747 1822 7.049799 TGGGTTGTTAAGAAAGGATTCAAAG 57.950 36.000 0.00 0.00 38.06 2.77
1748 1823 6.609616 TGGGTTGTTAAGAAAGGATTCAAAGT 59.390 34.615 0.00 0.00 38.06 2.66
1749 1824 7.125053 TGGGTTGTTAAGAAAGGATTCAAAGTT 59.875 33.333 0.00 0.00 38.06 2.66
1750 1825 8.635328 GGGTTGTTAAGAAAGGATTCAAAGTTA 58.365 33.333 0.00 0.00 38.06 2.24
1751 1826 9.459640 GGTTGTTAAGAAAGGATTCAAAGTTAC 57.540 33.333 0.00 0.00 38.06 2.50
1752 1827 9.459640 GTTGTTAAGAAAGGATTCAAAGTTACC 57.540 33.333 0.00 0.00 38.06 2.85
1753 1828 8.173542 TGTTAAGAAAGGATTCAAAGTTACCC 57.826 34.615 0.00 0.00 38.06 3.69
1754 1829 7.231925 TGTTAAGAAAGGATTCAAAGTTACCCC 59.768 37.037 0.00 0.00 38.06 4.95
1755 1830 5.600669 AGAAAGGATTCAAAGTTACCCCT 57.399 39.130 0.00 0.00 38.06 4.79
1756 1831 6.713731 AGAAAGGATTCAAAGTTACCCCTA 57.286 37.500 0.00 0.00 38.06 3.53
1757 1832 6.722328 AGAAAGGATTCAAAGTTACCCCTAG 58.278 40.000 0.00 0.00 38.06 3.02
1758 1833 5.452341 AAGGATTCAAAGTTACCCCTAGG 57.548 43.478 0.06 0.06 40.04 3.02
1759 1834 6.523670 GAAAGGATTCAAAGTTACCCCTAGGT 60.524 42.308 8.29 0.00 41.68 3.08
1760 1835 8.496454 GAAAGGATTCAAAGTTACCCCTAGGTG 61.496 44.444 8.29 0.00 40.19 4.00
1772 1847 3.235200 CCCCTAGGTGAACTCTATGAGG 58.765 54.545 8.29 0.00 33.35 3.86
1773 1848 3.374318 CCCCTAGGTGAACTCTATGAGGT 60.374 52.174 8.29 0.00 33.35 3.85
1774 1849 4.290942 CCCTAGGTGAACTCTATGAGGTT 58.709 47.826 8.29 0.00 33.35 3.50
1775 1850 4.342665 CCCTAGGTGAACTCTATGAGGTTC 59.657 50.000 8.29 0.00 41.28 3.62
1776 1851 4.036971 CCTAGGTGAACTCTATGAGGTTCG 59.963 50.000 0.00 0.00 43.10 3.95
1777 1852 3.698289 AGGTGAACTCTATGAGGTTCGA 58.302 45.455 0.00 0.00 43.10 3.71
1778 1853 4.087182 AGGTGAACTCTATGAGGTTCGAA 58.913 43.478 0.00 0.00 43.10 3.71
1779 1854 4.712337 AGGTGAACTCTATGAGGTTCGAAT 59.288 41.667 0.00 0.00 43.10 3.34
1780 1855 5.044558 GGTGAACTCTATGAGGTTCGAATC 58.955 45.833 0.00 0.00 43.10 2.52
1781 1856 5.044558 GTGAACTCTATGAGGTTCGAATCC 58.955 45.833 4.40 6.73 43.10 3.01
1782 1857 4.099573 TGAACTCTATGAGGTTCGAATCCC 59.900 45.833 4.40 0.05 43.10 3.85
1783 1858 2.966516 ACTCTATGAGGTTCGAATCCCC 59.033 50.000 4.40 0.00 33.35 4.81
1784 1859 3.235200 CTCTATGAGGTTCGAATCCCCT 58.765 50.000 4.40 5.03 0.00 4.79
1785 1860 3.231818 TCTATGAGGTTCGAATCCCCTC 58.768 50.000 20.88 20.88 44.16 4.30
1786 1861 2.182516 ATGAGGTTCGAATCCCCTCT 57.817 50.000 25.31 13.61 44.21 3.69
1787 1862 1.952621 TGAGGTTCGAATCCCCTCTT 58.047 50.000 25.31 0.62 44.21 2.85
1788 1863 1.555075 TGAGGTTCGAATCCCCTCTTG 59.445 52.381 25.31 0.00 44.21 3.02
1789 1864 1.555533 GAGGTTCGAATCCCCTCTTGT 59.444 52.381 20.56 0.00 41.31 3.16
1790 1865 1.985895 AGGTTCGAATCCCCTCTTGTT 59.014 47.619 4.40 0.00 0.00 2.83
1791 1866 2.027100 AGGTTCGAATCCCCTCTTGTTC 60.027 50.000 4.40 0.00 0.00 3.18
1792 1867 2.357075 GTTCGAATCCCCTCTTGTTCC 58.643 52.381 0.00 0.00 0.00 3.62
1793 1868 1.651737 TCGAATCCCCTCTTGTTCCA 58.348 50.000 0.00 0.00 0.00 3.53
1794 1869 1.278127 TCGAATCCCCTCTTGTTCCAC 59.722 52.381 0.00 0.00 0.00 4.02
1795 1870 1.003118 CGAATCCCCTCTTGTTCCACA 59.997 52.381 0.00 0.00 0.00 4.17
1796 1871 2.552155 CGAATCCCCTCTTGTTCCACAA 60.552 50.000 0.00 0.00 36.54 3.33
1860 1935 1.600164 GCGTTCGTTTGGGGTAAAACC 60.600 52.381 0.00 0.00 36.83 3.27
1873 1948 3.208594 GGTAAAACCAACGAACCAGACT 58.791 45.455 0.00 0.00 38.42 3.24
2159 2275 3.330720 CAGCCCCTTTCCCTCGGT 61.331 66.667 0.00 0.00 0.00 4.69
2188 2305 1.259609 CTACCAACCACGACCACCTA 58.740 55.000 0.00 0.00 0.00 3.08
2217 2334 4.460683 CGCCGACCGGATTTGGGA 62.461 66.667 9.46 0.00 37.50 4.37
2290 2408 3.625897 CTGGACGGACACCTGGCA 61.626 66.667 0.00 0.00 0.00 4.92
2369 2495 2.357034 CCGTCGGTGGTCCTGTTG 60.357 66.667 2.08 0.00 0.00 3.33
2371 2497 2.863346 CGTCGGTGGTCCTGTTGGA 61.863 63.158 0.00 0.00 40.69 3.53
2372 2498 1.448497 GTCGGTGGTCCTGTTGGAA 59.552 57.895 0.00 0.00 45.18 3.53
2374 2500 0.768622 TCGGTGGTCCTGTTGGAAAT 59.231 50.000 0.00 0.00 45.18 2.17
2375 2501 1.979308 TCGGTGGTCCTGTTGGAAATA 59.021 47.619 0.00 0.00 45.18 1.40
2376 2502 2.574369 TCGGTGGTCCTGTTGGAAATAT 59.426 45.455 0.00 0.00 45.18 1.28
2377 2503 2.682856 CGGTGGTCCTGTTGGAAATATG 59.317 50.000 0.00 0.00 45.18 1.78
2378 2504 2.427095 GGTGGTCCTGTTGGAAATATGC 59.573 50.000 0.00 0.00 45.18 3.14
2379 2505 2.427095 GTGGTCCTGTTGGAAATATGCC 59.573 50.000 0.00 0.00 45.18 4.40
2380 2506 2.031870 GGTCCTGTTGGAAATATGCCC 58.968 52.381 0.00 0.00 45.18 5.36
2381 2507 2.358195 GGTCCTGTTGGAAATATGCCCT 60.358 50.000 0.00 0.00 45.18 5.19
2382 2508 3.117663 GGTCCTGTTGGAAATATGCCCTA 60.118 47.826 0.00 0.00 45.18 3.53
2383 2509 4.137543 GTCCTGTTGGAAATATGCCCTAG 58.862 47.826 0.00 0.00 45.18 3.02
2384 2510 4.044308 TCCTGTTGGAAATATGCCCTAGA 58.956 43.478 0.00 0.00 39.87 2.43
2385 2511 4.103153 TCCTGTTGGAAATATGCCCTAGAG 59.897 45.833 0.00 0.00 39.87 2.43
2386 2512 4.392940 CTGTTGGAAATATGCCCTAGAGG 58.607 47.826 0.00 0.00 39.47 3.69
2387 2513 4.044308 TGTTGGAAATATGCCCTAGAGGA 58.956 43.478 0.00 0.00 38.24 3.71
2388 2514 4.476846 TGTTGGAAATATGCCCTAGAGGAA 59.523 41.667 0.00 0.00 38.24 3.36
2389 2515 5.044476 TGTTGGAAATATGCCCTAGAGGAAA 60.044 40.000 0.00 0.00 38.24 3.13
2390 2516 5.930209 TGGAAATATGCCCTAGAGGAAAT 57.070 39.130 0.00 0.00 38.24 2.17
2391 2517 7.147213 TGTTGGAAATATGCCCTAGAGGAAATA 60.147 37.037 0.00 0.00 38.24 1.40
2392 2518 7.401060 TGGAAATATGCCCTAGAGGAAATAA 57.599 36.000 0.00 0.00 38.24 1.40
2393 2519 8.000171 TGGAAATATGCCCTAGAGGAAATAAT 58.000 34.615 0.00 0.00 38.24 1.28
2394 2520 9.122954 TGGAAATATGCCCTAGAGGAAATAATA 57.877 33.333 0.00 0.00 38.24 0.98
2395 2521 9.975218 GGAAATATGCCCTAGAGGAAATAATAA 57.025 33.333 0.00 0.00 38.24 1.40
2400 2526 8.697507 ATGCCCTAGAGGAAATAATAAAAGTG 57.302 34.615 0.00 0.00 38.24 3.16
2401 2527 7.639378 TGCCCTAGAGGAAATAATAAAAGTGT 58.361 34.615 0.00 0.00 38.24 3.55
2402 2528 8.113462 TGCCCTAGAGGAAATAATAAAAGTGTT 58.887 33.333 0.00 0.00 38.24 3.32
2403 2529 9.623000 GCCCTAGAGGAAATAATAAAAGTGTTA 57.377 33.333 0.00 0.00 38.24 2.41
2464 2590 8.948631 ATTCATGCTATAACTGTATTATCCGG 57.051 34.615 0.00 0.00 0.00 5.14
2465 2591 7.712204 TCATGCTATAACTGTATTATCCGGA 57.288 36.000 6.61 6.61 0.00 5.14
2466 2592 8.129496 TCATGCTATAACTGTATTATCCGGAA 57.871 34.615 9.01 0.00 0.00 4.30
2467 2593 8.590204 TCATGCTATAACTGTATTATCCGGAAA 58.410 33.333 9.01 4.74 0.00 3.13
2468 2594 9.383519 CATGCTATAACTGTATTATCCGGAAAT 57.616 33.333 9.01 12.31 0.00 2.17
2469 2595 8.997621 TGCTATAACTGTATTATCCGGAAATC 57.002 34.615 9.01 5.33 0.00 2.17
2470 2596 7.758076 TGCTATAACTGTATTATCCGGAAATCG 59.242 37.037 9.01 5.25 38.88 3.34
2471 2597 7.758528 GCTATAACTGTATTATCCGGAAATCGT 59.241 37.037 9.01 5.81 37.11 3.73
2476 2602 8.976986 ACTGTATTATCCGGAAATCGTAATAC 57.023 34.615 25.06 25.06 40.20 1.89
2477 2603 8.579006 ACTGTATTATCCGGAAATCGTAATACA 58.421 33.333 28.89 28.89 43.27 2.29
2478 2604 8.746922 TGTATTATCCGGAAATCGTAATACAC 57.253 34.615 28.04 16.29 42.13 2.90
2494 2620 7.979037 CGTAATACACGTGTGAATACATAGAC 58.021 38.462 30.83 14.41 45.82 2.59
2495 2621 7.112565 CGTAATACACGTGTGAATACATAGACC 59.887 40.741 30.83 6.57 45.82 3.85
2496 2622 4.794278 ACACGTGTGAATACATAGACCA 57.206 40.909 22.71 0.00 39.39 4.02
2497 2623 4.491676 ACACGTGTGAATACATAGACCAC 58.508 43.478 22.71 0.00 39.39 4.16
2498 2624 4.021807 ACACGTGTGAATACATAGACCACA 60.022 41.667 22.71 0.00 39.39 4.17
2499 2625 4.926832 CACGTGTGAATACATAGACCACAA 59.073 41.667 7.58 0.00 39.13 3.33
2500 2626 5.580691 CACGTGTGAATACATAGACCACAAT 59.419 40.000 7.58 0.00 39.13 2.71
2501 2627 6.754675 CACGTGTGAATACATAGACCACAATA 59.245 38.462 7.58 0.00 39.13 1.90
2502 2628 7.438160 CACGTGTGAATACATAGACCACAATAT 59.562 37.037 7.58 0.00 39.13 1.28
2503 2629 7.438160 ACGTGTGAATACATAGACCACAATATG 59.562 37.037 0.00 0.00 39.13 1.78
2504 2630 7.438160 CGTGTGAATACATAGACCACAATATGT 59.562 37.037 0.00 3.60 43.31 2.29
2505 2631 8.765219 GTGTGAATACATAGACCACAATATGTC 58.235 37.037 0.00 0.00 40.78 3.06
2506 2632 7.931407 TGTGAATACATAGACCACAATATGTCC 59.069 37.037 1.37 0.00 40.78 4.02
2507 2633 7.387948 GTGAATACATAGACCACAATATGTCCC 59.612 40.741 1.37 0.00 40.78 4.46
2508 2634 7.292356 TGAATACATAGACCACAATATGTCCCT 59.708 37.037 1.37 0.00 40.78 4.20
2509 2635 8.736097 AATACATAGACCACAATATGTCCCTA 57.264 34.615 1.37 0.00 40.78 3.53
2510 2636 6.672266 ACATAGACCACAATATGTCCCTAG 57.328 41.667 0.00 0.00 37.98 3.02
2511 2637 6.143915 ACATAGACCACAATATGTCCCTAGT 58.856 40.000 0.00 0.00 37.98 2.57
2512 2638 6.042093 ACATAGACCACAATATGTCCCTAGTG 59.958 42.308 0.00 0.00 37.98 2.74
2513 2639 4.620723 AGACCACAATATGTCCCTAGTGA 58.379 43.478 0.00 0.00 31.76 3.41
2514 2640 4.651503 AGACCACAATATGTCCCTAGTGAG 59.348 45.833 0.00 0.00 31.76 3.51
2515 2641 4.362677 ACCACAATATGTCCCTAGTGAGT 58.637 43.478 0.00 0.00 0.00 3.41
2516 2642 4.406003 ACCACAATATGTCCCTAGTGAGTC 59.594 45.833 0.00 0.00 0.00 3.36
2517 2643 4.651503 CCACAATATGTCCCTAGTGAGTCT 59.348 45.833 0.00 0.00 0.00 3.24
2518 2644 5.221342 CCACAATATGTCCCTAGTGAGTCTC 60.221 48.000 0.00 0.00 0.00 3.36
2519 2645 5.596361 CACAATATGTCCCTAGTGAGTCTCT 59.404 44.000 0.65 0.00 0.00 3.10
2520 2646 6.773200 CACAATATGTCCCTAGTGAGTCTCTA 59.227 42.308 0.65 2.14 0.00 2.43
2521 2647 7.001674 ACAATATGTCCCTAGTGAGTCTCTAG 58.998 42.308 18.42 18.42 35.86 2.43
2522 2648 6.773583 ATATGTCCCTAGTGAGTCTCTAGT 57.226 41.667 21.85 10.11 34.72 2.57
2523 2649 4.931027 TGTCCCTAGTGAGTCTCTAGTT 57.069 45.455 21.85 0.00 34.72 2.24
2524 2650 4.590918 TGTCCCTAGTGAGTCTCTAGTTG 58.409 47.826 21.85 14.98 34.72 3.16
2525 2651 4.288887 TGTCCCTAGTGAGTCTCTAGTTGA 59.711 45.833 21.85 16.49 34.72 3.18
2526 2652 4.637091 GTCCCTAGTGAGTCTCTAGTTGAC 59.363 50.000 21.85 21.46 34.72 3.18
2527 2653 4.536888 TCCCTAGTGAGTCTCTAGTTGACT 59.463 45.833 21.85 16.75 46.17 3.41
2528 2654 5.725338 TCCCTAGTGAGTCTCTAGTTGACTA 59.275 44.000 21.85 5.75 43.88 2.59
2529 2655 6.053005 CCCTAGTGAGTCTCTAGTTGACTAG 58.947 48.000 21.85 11.14 43.88 2.57
2530 2656 5.526111 CCTAGTGAGTCTCTAGTTGACTAGC 59.474 48.000 21.85 13.31 43.88 3.42
2531 2657 5.174037 AGTGAGTCTCTAGTTGACTAGCT 57.826 43.478 16.76 14.68 43.88 3.32
2532 2658 5.183228 AGTGAGTCTCTAGTTGACTAGCTC 58.817 45.833 16.76 12.79 43.88 4.09
2533 2659 4.033587 GTGAGTCTCTAGTTGACTAGCTCG 59.966 50.000 16.76 0.00 43.88 5.03
2534 2660 4.186159 GAGTCTCTAGTTGACTAGCTCGT 58.814 47.826 16.76 0.00 43.88 4.18
2535 2661 4.581868 AGTCTCTAGTTGACTAGCTCGTT 58.418 43.478 15.73 0.00 44.24 3.85
2536 2662 4.393680 AGTCTCTAGTTGACTAGCTCGTTG 59.606 45.833 15.73 1.13 44.24 4.10
2537 2663 4.154556 GTCTCTAGTTGACTAGCTCGTTGT 59.845 45.833 12.30 0.00 44.24 3.32
2538 2664 4.154375 TCTCTAGTTGACTAGCTCGTTGTG 59.846 45.833 12.30 0.00 44.24 3.33
2539 2665 4.070009 TCTAGTTGACTAGCTCGTTGTGA 58.930 43.478 12.30 0.00 44.24 3.58
2540 2666 3.944055 AGTTGACTAGCTCGTTGTGAT 57.056 42.857 0.00 0.00 0.00 3.06
2541 2667 3.839293 AGTTGACTAGCTCGTTGTGATC 58.161 45.455 0.00 0.00 0.00 2.92
2542 2668 3.255888 AGTTGACTAGCTCGTTGTGATCA 59.744 43.478 0.00 0.00 0.00 2.92
2543 2669 3.934457 TGACTAGCTCGTTGTGATCAA 57.066 42.857 0.00 0.00 0.00 2.57
2544 2670 8.771523 CTAGTTGACTAGCTCGTTGTGATCAAC 61.772 44.444 0.00 9.17 42.66 3.18
2557 2683 5.682234 TGTGATCAACAGATAGTCATGGT 57.318 39.130 0.00 0.00 33.78 3.55
2558 2684 6.053632 TGTGATCAACAGATAGTCATGGTT 57.946 37.500 0.00 0.00 33.78 3.67
2559 2685 6.475504 TGTGATCAACAGATAGTCATGGTTT 58.524 36.000 0.00 0.00 33.78 3.27
2560 2686 6.595326 TGTGATCAACAGATAGTCATGGTTTC 59.405 38.462 0.00 0.00 33.78 2.78
2561 2687 6.037610 GTGATCAACAGATAGTCATGGTTTCC 59.962 42.308 0.00 0.00 0.00 3.13
2562 2688 5.762179 TCAACAGATAGTCATGGTTTCCT 57.238 39.130 0.00 0.00 0.00 3.36
2563 2689 5.491070 TCAACAGATAGTCATGGTTTCCTG 58.509 41.667 0.00 0.00 0.00 3.86
2564 2690 4.494091 ACAGATAGTCATGGTTTCCTGG 57.506 45.455 0.00 0.00 0.00 4.45
2565 2691 3.209410 CAGATAGTCATGGTTTCCTGGC 58.791 50.000 0.00 0.00 0.00 4.85
2566 2692 3.118112 CAGATAGTCATGGTTTCCTGGCT 60.118 47.826 0.00 0.00 0.00 4.75
2567 2693 4.101585 CAGATAGTCATGGTTTCCTGGCTA 59.898 45.833 0.00 0.00 34.35 3.93
2568 2694 4.910304 AGATAGTCATGGTTTCCTGGCTAT 59.090 41.667 10.00 10.00 41.67 2.97
2569 2695 3.287867 AGTCATGGTTTCCTGGCTATG 57.712 47.619 0.00 0.00 0.00 2.23
2570 2696 2.092212 AGTCATGGTTTCCTGGCTATGG 60.092 50.000 0.00 0.00 0.00 2.74
2571 2697 2.092429 GTCATGGTTTCCTGGCTATGGA 60.092 50.000 0.00 0.00 0.00 3.41
2572 2698 2.092429 TCATGGTTTCCTGGCTATGGAC 60.092 50.000 0.00 0.00 32.65 4.02
2573 2699 1.367346 TGGTTTCCTGGCTATGGACA 58.633 50.000 0.00 0.00 32.65 4.02
2574 2700 1.922447 TGGTTTCCTGGCTATGGACAT 59.078 47.619 0.00 0.00 32.65 3.06
2575 2701 2.311542 TGGTTTCCTGGCTATGGACATT 59.688 45.455 0.00 0.00 32.65 2.71
2576 2702 2.689983 GGTTTCCTGGCTATGGACATTG 59.310 50.000 0.00 0.00 32.65 2.82
2577 2703 2.689983 GTTTCCTGGCTATGGACATTGG 59.310 50.000 0.00 0.00 32.65 3.16
2578 2704 1.891933 TCCTGGCTATGGACATTGGA 58.108 50.000 0.00 0.00 0.00 3.53
2579 2705 2.421725 TCCTGGCTATGGACATTGGAT 58.578 47.619 0.00 0.00 0.00 3.41
2580 2706 2.107031 TCCTGGCTATGGACATTGGATG 59.893 50.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 6.113411 CGGTATAAAGTCAGGGAAACATTCT 58.887 40.000 0.00 0.00 0.00 2.40
69 70 3.075005 TCCCTCACTAGTGCCGCC 61.075 66.667 18.45 0.00 0.00 6.13
366 370 4.442612 GGGGAGGTAGGTTTCGAAGAATAC 60.443 50.000 0.00 2.84 45.90 1.89
500 507 1.686587 TCACCGGTATCTGCATCGATT 59.313 47.619 6.87 0.00 0.00 3.34
530 537 5.011090 ACTTGCTGAAGTTTCTTTTTCCC 57.989 39.130 0.00 0.00 39.56 3.97
550 557 9.694137 GTAGATAAGAAATCAGCGGTTATAACT 57.306 33.333 15.05 0.00 0.00 2.24
784 826 1.295792 TCGCGAAAAGTGAAGCTGTT 58.704 45.000 6.20 0.00 36.26 3.16
883 933 1.341383 GCAATGGAGGAATGGGTGAGT 60.341 52.381 0.00 0.00 0.00 3.41
888 938 1.690352 GAATGGCAATGGAGGAATGGG 59.310 52.381 0.00 0.00 0.00 4.00
893 943 0.327924 ACGTGAATGGCAATGGAGGA 59.672 50.000 0.00 0.00 0.00 3.71
915 967 1.666189 GGCGTTAATGGCAAGAGAGAC 59.334 52.381 15.87 0.00 0.00 3.36
920 972 1.647346 CGTAGGCGTTAATGGCAAGA 58.353 50.000 21.91 5.36 36.77 3.02
921 973 0.027586 GCGTAGGCGTTAATGGCAAG 59.972 55.000 21.91 13.39 40.81 4.01
924 976 0.730840 AAAGCGTAGGCGTTAATGGC 59.269 50.000 13.14 13.14 46.35 4.40
925 977 2.004017 TGAAAGCGTAGGCGTTAATGG 58.996 47.619 8.55 0.00 46.35 3.16
933 991 0.931005 CGATCCTTGAAAGCGTAGGC 59.069 55.000 0.00 0.00 40.37 3.93
940 998 1.714794 ACGTGCTCGATCCTTGAAAG 58.285 50.000 16.04 0.00 40.62 2.62
989 1052 0.319900 CGAAATCATCCCGGCGAGAT 60.320 55.000 9.30 1.99 0.00 2.75
1041 1104 0.765903 GATCCTGATCCTGGGCCTCA 60.766 60.000 4.53 0.00 31.76 3.86
1191 1260 1.985116 GTTCTCCTGGAGGTCGGCT 60.985 63.158 23.00 0.00 36.34 5.52
1236 1305 0.514691 GGCAGCACTTCAAGAACTCG 59.485 55.000 0.00 0.00 0.00 4.18
1310 1379 3.196469 TGAGGAAGGTGCAAGTGATCTAG 59.804 47.826 0.00 0.00 0.00 2.43
1311 1380 3.173151 TGAGGAAGGTGCAAGTGATCTA 58.827 45.455 0.00 0.00 0.00 1.98
1318 1387 4.015084 AGATTGAATGAGGAAGGTGCAAG 58.985 43.478 0.00 0.00 0.00 4.01
1319 1388 4.012374 GAGATTGAATGAGGAAGGTGCAA 58.988 43.478 0.00 0.00 0.00 4.08
1345 1416 3.305608 GCTCAAGCCAAGCAACAATTAGT 60.306 43.478 0.00 0.00 39.61 2.24
1348 1419 1.690352 AGCTCAAGCCAAGCAACAATT 59.310 42.857 0.00 0.00 42.35 2.32
1355 1426 1.401199 GAATCTCAGCTCAAGCCAAGC 59.599 52.381 0.00 0.00 43.38 4.01
1390 1461 2.293170 GCTCTCCCCTGCAGAATTAAC 58.707 52.381 17.39 0.00 0.00 2.01
1394 1465 0.255318 CTTGCTCTCCCCTGCAGAAT 59.745 55.000 17.39 0.00 40.46 2.40
1426 1497 4.664677 GCTGACACCGGCACTCGT 62.665 66.667 0.00 0.00 44.05 4.18
1590 1661 6.649155 TGCAAGTACAGCAAGGATCTAATTA 58.351 36.000 10.16 0.00 39.39 1.40
1591 1662 5.500234 TGCAAGTACAGCAAGGATCTAATT 58.500 37.500 10.16 0.00 39.39 1.40
1617 1692 6.313519 TCATCCTTAGTTTATCACTGGCTT 57.686 37.500 0.00 0.00 35.97 4.35
1659 1734 9.753674 TGAAATTTGTCCTAACTAATCATCCTT 57.246 29.630 0.00 0.00 30.97 3.36
1660 1735 9.753674 TTGAAATTTGTCCTAACTAATCATCCT 57.246 29.630 0.00 0.00 30.97 3.24
1664 1739 9.010029 GGACTTGAAATTTGTCCTAACTAATCA 57.990 33.333 15.56 0.00 44.84 2.57
1682 1757 9.841295 AGTTGTACTACAAATTTAGGACTTGAA 57.159 29.630 10.09 0.00 40.15 2.69
1683 1758 9.268268 CAGTTGTACTACAAATTTAGGACTTGA 57.732 33.333 10.09 0.00 40.15 3.02
1684 1759 9.052759 ACAGTTGTACTACAAATTTAGGACTTG 57.947 33.333 10.09 4.23 40.15 3.16
1686 1761 9.702494 GTACAGTTGTACTACAAATTTAGGACT 57.298 33.333 13.72 0.00 45.47 3.85
1702 1777 5.302360 CCAAAGCCTACTTGTACAGTTGTA 58.698 41.667 0.00 0.91 36.88 2.41
1703 1778 4.134563 CCAAAGCCTACTTGTACAGTTGT 58.865 43.478 0.00 0.00 36.88 3.32
1704 1779 3.502211 CCCAAAGCCTACTTGTACAGTTG 59.498 47.826 0.00 0.00 36.88 3.16
1705 1780 3.137728 ACCCAAAGCCTACTTGTACAGTT 59.862 43.478 0.00 0.00 36.88 3.16
1706 1781 2.709397 ACCCAAAGCCTACTTGTACAGT 59.291 45.455 0.00 0.00 39.87 3.55
1707 1782 3.418684 ACCCAAAGCCTACTTGTACAG 57.581 47.619 0.00 0.00 35.85 2.74
1708 1783 3.117813 ACAACCCAAAGCCTACTTGTACA 60.118 43.478 0.00 0.00 35.85 2.90
1709 1784 3.483421 ACAACCCAAAGCCTACTTGTAC 58.517 45.455 0.00 0.00 35.85 2.90
1710 1785 3.868619 ACAACCCAAAGCCTACTTGTA 57.131 42.857 0.00 0.00 35.85 2.41
1711 1786 2.748209 ACAACCCAAAGCCTACTTGT 57.252 45.000 0.00 0.00 35.85 3.16
1712 1787 4.825085 TCTTAACAACCCAAAGCCTACTTG 59.175 41.667 0.00 0.00 35.85 3.16
1713 1788 5.056553 TCTTAACAACCCAAAGCCTACTT 57.943 39.130 0.00 0.00 37.90 2.24
1714 1789 4.717279 TCTTAACAACCCAAAGCCTACT 57.283 40.909 0.00 0.00 0.00 2.57
1715 1790 5.278808 CCTTTCTTAACAACCCAAAGCCTAC 60.279 44.000 0.00 0.00 0.00 3.18
1716 1791 4.830600 CCTTTCTTAACAACCCAAAGCCTA 59.169 41.667 0.00 0.00 0.00 3.93
1717 1792 3.641436 CCTTTCTTAACAACCCAAAGCCT 59.359 43.478 0.00 0.00 0.00 4.58
1718 1793 3.639561 TCCTTTCTTAACAACCCAAAGCC 59.360 43.478 0.00 0.00 0.00 4.35
1719 1794 4.929819 TCCTTTCTTAACAACCCAAAGC 57.070 40.909 0.00 0.00 0.00 3.51
1720 1795 7.049799 TGAATCCTTTCTTAACAACCCAAAG 57.950 36.000 0.00 0.00 32.78 2.77
1721 1796 7.425224 TTGAATCCTTTCTTAACAACCCAAA 57.575 32.000 0.00 0.00 32.78 3.28
1722 1797 7.125053 ACTTTGAATCCTTTCTTAACAACCCAA 59.875 33.333 0.00 0.00 32.78 4.12
1723 1798 6.609616 ACTTTGAATCCTTTCTTAACAACCCA 59.390 34.615 0.00 0.00 32.78 4.51
1724 1799 7.050970 ACTTTGAATCCTTTCTTAACAACCC 57.949 36.000 0.00 0.00 32.78 4.11
1725 1800 9.459640 GTAACTTTGAATCCTTTCTTAACAACC 57.540 33.333 0.00 0.00 32.78 3.77
1726 1801 9.459640 GGTAACTTTGAATCCTTTCTTAACAAC 57.540 33.333 0.00 0.00 32.78 3.32
1727 1802 8.635328 GGGTAACTTTGAATCCTTTCTTAACAA 58.365 33.333 0.00 0.00 32.78 2.83
1728 1803 7.231925 GGGGTAACTTTGAATCCTTTCTTAACA 59.768 37.037 0.00 0.00 32.78 2.41
1729 1804 7.450634 AGGGGTAACTTTGAATCCTTTCTTAAC 59.549 37.037 0.00 0.00 32.78 2.01
1730 1805 7.532199 AGGGGTAACTTTGAATCCTTTCTTAA 58.468 34.615 0.00 0.00 32.78 1.85
1731 1806 7.098845 AGGGGTAACTTTGAATCCTTTCTTA 57.901 36.000 0.00 0.00 32.78 2.10
1732 1807 5.965486 AGGGGTAACTTTGAATCCTTTCTT 58.035 37.500 0.00 0.00 32.78 2.52
1733 1808 5.600669 AGGGGTAACTTTGAATCCTTTCT 57.399 39.130 0.00 0.00 32.78 2.52
1734 1809 5.886474 CCTAGGGGTAACTTTGAATCCTTTC 59.114 44.000 0.00 0.00 0.00 2.62
1735 1810 5.315109 ACCTAGGGGTAACTTTGAATCCTTT 59.685 40.000 14.81 0.00 45.32 3.11
1736 1811 4.856182 ACCTAGGGGTAACTTTGAATCCTT 59.144 41.667 14.81 0.00 45.32 3.36
1737 1812 4.227527 CACCTAGGGGTAACTTTGAATCCT 59.772 45.833 14.81 0.00 45.41 3.24
1738 1813 4.226620 TCACCTAGGGGTAACTTTGAATCC 59.773 45.833 11.80 0.00 45.41 3.01
1739 1814 5.431179 TCACCTAGGGGTAACTTTGAATC 57.569 43.478 11.80 0.00 45.41 2.52
1740 1815 5.312443 AGTTCACCTAGGGGTAACTTTGAAT 59.688 40.000 17.99 4.37 45.41 2.57
1741 1816 4.661709 AGTTCACCTAGGGGTAACTTTGAA 59.338 41.667 17.99 11.48 45.41 2.69
1742 1817 4.237018 AGTTCACCTAGGGGTAACTTTGA 58.763 43.478 17.99 6.68 45.41 2.69
1743 1818 4.286291 AGAGTTCACCTAGGGGTAACTTTG 59.714 45.833 22.14 7.61 45.41 2.77
1744 1819 4.500452 AGAGTTCACCTAGGGGTAACTTT 58.500 43.478 22.14 16.79 45.41 2.66
1745 1820 4.143406 AGAGTTCACCTAGGGGTAACTT 57.857 45.455 22.14 13.43 45.41 2.66
1746 1821 3.848978 AGAGTTCACCTAGGGGTAACT 57.151 47.619 21.68 21.68 45.41 2.24
1747 1822 5.206587 TCATAGAGTTCACCTAGGGGTAAC 58.793 45.833 11.80 13.75 45.41 2.50
1748 1823 5.455872 CTCATAGAGTTCACCTAGGGGTAA 58.544 45.833 11.80 1.07 45.41 2.85
1749 1824 4.140994 CCTCATAGAGTTCACCTAGGGGTA 60.141 50.000 11.80 0.00 45.41 3.69
1751 1826 3.235200 CCTCATAGAGTTCACCTAGGGG 58.765 54.545 14.81 9.88 38.88 4.79
1752 1827 3.917300 ACCTCATAGAGTTCACCTAGGG 58.083 50.000 14.81 2.03 0.00 3.53
1753 1828 4.036971 CGAACCTCATAGAGTTCACCTAGG 59.963 50.000 7.41 7.41 0.00 3.02
1754 1829 4.882427 TCGAACCTCATAGAGTTCACCTAG 59.118 45.833 4.03 0.00 0.00 3.02
1755 1830 4.851843 TCGAACCTCATAGAGTTCACCTA 58.148 43.478 4.03 0.00 0.00 3.08
1756 1831 3.698289 TCGAACCTCATAGAGTTCACCT 58.302 45.455 4.03 0.00 0.00 4.00
1757 1832 4.451629 TTCGAACCTCATAGAGTTCACC 57.548 45.455 0.00 0.00 0.00 4.02
1758 1833 5.044558 GGATTCGAACCTCATAGAGTTCAC 58.955 45.833 0.00 0.00 0.00 3.18
1759 1834 4.099573 GGGATTCGAACCTCATAGAGTTCA 59.900 45.833 0.00 0.00 0.00 3.18
1760 1835 4.501743 GGGGATTCGAACCTCATAGAGTTC 60.502 50.000 0.00 0.00 0.00 3.01
1761 1836 3.388350 GGGGATTCGAACCTCATAGAGTT 59.612 47.826 0.00 0.00 0.00 3.01
1762 1837 2.966516 GGGGATTCGAACCTCATAGAGT 59.033 50.000 0.00 0.00 0.00 3.24
1763 1838 3.235200 AGGGGATTCGAACCTCATAGAG 58.765 50.000 15.95 0.00 0.00 2.43
1764 1839 3.330126 AGGGGATTCGAACCTCATAGA 57.670 47.619 15.95 0.00 0.00 1.98
1770 1845 1.657804 ACAAGAGGGGATTCGAACCT 58.342 50.000 0.00 2.03 37.31 3.50
1771 1846 2.357075 GAACAAGAGGGGATTCGAACC 58.643 52.381 0.00 4.00 0.00 3.62
1772 1847 2.290071 TGGAACAAGAGGGGATTCGAAC 60.290 50.000 0.00 0.00 31.92 3.95
1773 1848 1.982226 TGGAACAAGAGGGGATTCGAA 59.018 47.619 0.00 0.00 31.92 3.71
1774 1849 1.278127 GTGGAACAAGAGGGGATTCGA 59.722 52.381 0.00 0.00 44.16 3.71
1775 1850 1.739067 GTGGAACAAGAGGGGATTCG 58.261 55.000 0.00 0.00 44.16 3.34
1786 1861 1.953686 GCCTAAGCTGTTGTGGAACAA 59.046 47.619 0.00 0.00 45.89 2.83
1787 1862 1.604604 GCCTAAGCTGTTGTGGAACA 58.395 50.000 0.00 0.00 40.34 3.18
1788 1863 0.881796 GGCCTAAGCTGTTGTGGAAC 59.118 55.000 0.00 0.00 39.73 3.62
1789 1864 0.476338 TGGCCTAAGCTGTTGTGGAA 59.524 50.000 3.32 0.00 39.73 3.53
1790 1865 0.476338 TTGGCCTAAGCTGTTGTGGA 59.524 50.000 3.32 0.00 39.73 4.02
1791 1866 0.598065 GTTGGCCTAAGCTGTTGTGG 59.402 55.000 3.32 0.00 39.73 4.17
1792 1867 1.537202 GAGTTGGCCTAAGCTGTTGTG 59.463 52.381 3.32 0.00 39.73 3.33
1793 1868 1.545651 GGAGTTGGCCTAAGCTGTTGT 60.546 52.381 3.32 0.00 39.73 3.32
1794 1869 1.168714 GGAGTTGGCCTAAGCTGTTG 58.831 55.000 3.32 0.00 39.73 3.33
1795 1870 0.771127 TGGAGTTGGCCTAAGCTGTT 59.229 50.000 3.32 0.00 39.73 3.16
1796 1871 0.036875 GTGGAGTTGGCCTAAGCTGT 59.963 55.000 3.32 0.00 39.73 4.40
1860 1935 1.227823 TGGGCAGTCTGGTTCGTTG 60.228 57.895 1.14 0.00 0.00 4.10
1912 1987 0.672401 GATGGGTCGAAAGCGGACAA 60.672 55.000 0.00 0.00 38.28 3.18
1991 2066 2.125961 GGGGAGGACACGCGTAGAT 61.126 63.158 13.44 0.00 0.00 1.98
2078 2159 0.905357 CGGTGAGGGGAAGAGTGAAT 59.095 55.000 0.00 0.00 0.00 2.57
2079 2160 1.827399 GCGGTGAGGGGAAGAGTGAA 61.827 60.000 0.00 0.00 0.00 3.18
2159 2275 2.656069 GGTTGGTAGCTCGAGGGCA 61.656 63.158 15.58 0.00 34.17 5.36
2188 2305 4.555709 TCGGCGGGTGTGCAAACT 62.556 61.111 7.21 0.00 36.28 2.66
2217 2334 0.611062 TCAAGACCGACCAGATCCGT 60.611 55.000 0.00 0.00 0.00 4.69
2270 2388 1.908793 CCAGGTGTCCGTCCAGTCT 60.909 63.158 0.00 0.00 0.00 3.24
2277 2395 2.847234 TTCCTGCCAGGTGTCCGT 60.847 61.111 11.27 0.00 36.53 4.69
2365 2491 4.044308 TCCTCTAGGGCATATTTCCAACA 58.956 43.478 0.00 0.00 35.41 3.33
2366 2492 4.706842 TCCTCTAGGGCATATTTCCAAC 57.293 45.455 0.00 0.00 35.41 3.77
2367 2493 5.725551 TTTCCTCTAGGGCATATTTCCAA 57.274 39.130 0.00 0.00 35.41 3.53
2369 2495 9.975218 TTATTATTTCCTCTAGGGCATATTTCC 57.025 33.333 0.00 0.00 35.41 3.13
2374 2500 9.793259 CACTTTTATTATTTCCTCTAGGGCATA 57.207 33.333 0.00 0.00 35.41 3.14
2375 2501 8.282256 ACACTTTTATTATTTCCTCTAGGGCAT 58.718 33.333 0.00 0.00 35.41 4.40
2376 2502 7.639378 ACACTTTTATTATTTCCTCTAGGGCA 58.361 34.615 0.00 0.00 35.41 5.36
2377 2503 8.521170 AACACTTTTATTATTTCCTCTAGGGC 57.479 34.615 0.00 0.00 35.41 5.19
2439 2565 8.758829 TCCGGATAATACAGTTATAGCATGAAT 58.241 33.333 0.00 0.00 0.00 2.57
2440 2566 8.129496 TCCGGATAATACAGTTATAGCATGAA 57.871 34.615 0.00 0.00 0.00 2.57
2441 2567 7.712204 TCCGGATAATACAGTTATAGCATGA 57.288 36.000 0.00 0.00 0.00 3.07
2442 2568 8.771920 TTTCCGGATAATACAGTTATAGCATG 57.228 34.615 4.15 0.00 0.00 4.06
2443 2569 9.601217 GATTTCCGGATAATACAGTTATAGCAT 57.399 33.333 4.15 0.00 0.00 3.79
2444 2570 7.758076 CGATTTCCGGATAATACAGTTATAGCA 59.242 37.037 4.15 0.00 33.91 3.49
2445 2571 7.758528 ACGATTTCCGGATAATACAGTTATAGC 59.241 37.037 4.15 0.00 43.93 2.97
2450 2576 9.415544 GTATTACGATTTCCGGATAATACAGTT 57.584 33.333 26.02 11.20 39.68 3.16
2451 2577 8.579006 TGTATTACGATTTCCGGATAATACAGT 58.421 33.333 28.04 20.31 41.92 3.55
2452 2578 8.857216 GTGTATTACGATTTCCGGATAATACAG 58.143 37.037 30.32 18.57 44.29 2.74
2453 2579 8.746922 GTGTATTACGATTTCCGGATAATACA 57.253 34.615 28.04 28.04 43.07 2.29
2470 2596 7.916977 TGGTCTATGTATTCACACGTGTATTAC 59.083 37.037 22.90 20.91 37.54 1.89
2471 2597 7.916977 GTGGTCTATGTATTCACACGTGTATTA 59.083 37.037 22.90 9.93 37.54 0.98
2472 2598 6.755141 GTGGTCTATGTATTCACACGTGTATT 59.245 38.462 22.90 11.42 37.54 1.89
2473 2599 6.127563 TGTGGTCTATGTATTCACACGTGTAT 60.128 38.462 22.90 14.96 37.54 2.29
2474 2600 5.183522 TGTGGTCTATGTATTCACACGTGTA 59.816 40.000 22.90 7.35 37.54 2.90
2475 2601 4.021807 TGTGGTCTATGTATTCACACGTGT 60.022 41.667 17.22 17.22 37.54 4.49
2476 2602 4.490743 TGTGGTCTATGTATTCACACGTG 58.509 43.478 15.48 15.48 37.54 4.49
2477 2603 4.794278 TGTGGTCTATGTATTCACACGT 57.206 40.909 0.00 0.00 37.54 4.49
2478 2604 7.438160 ACATATTGTGGTCTATGTATTCACACG 59.562 37.037 0.00 0.00 36.93 4.49
2479 2605 8.662781 ACATATTGTGGTCTATGTATTCACAC 57.337 34.615 0.00 0.00 36.93 3.82
2480 2606 7.931407 GGACATATTGTGGTCTATGTATTCACA 59.069 37.037 0.00 0.00 38.38 3.58
2481 2607 7.387948 GGGACATATTGTGGTCTATGTATTCAC 59.612 40.741 0.00 0.00 38.38 3.18
2482 2608 7.292356 AGGGACATATTGTGGTCTATGTATTCA 59.708 37.037 0.00 0.00 38.38 2.57
2483 2609 7.680730 AGGGACATATTGTGGTCTATGTATTC 58.319 38.462 0.00 0.00 38.38 1.75
2484 2610 7.633018 AGGGACATATTGTGGTCTATGTATT 57.367 36.000 0.00 0.00 38.38 1.89
2485 2611 7.956315 ACTAGGGACATATTGTGGTCTATGTAT 59.044 37.037 0.00 0.00 38.38 2.29
2486 2612 7.232737 CACTAGGGACATATTGTGGTCTATGTA 59.767 40.741 0.00 0.00 38.38 2.29
2487 2613 6.042093 CACTAGGGACATATTGTGGTCTATGT 59.958 42.308 0.00 0.00 40.38 2.29
2488 2614 6.267699 TCACTAGGGACATATTGTGGTCTATG 59.732 42.308 0.00 0.00 34.49 2.23
2489 2615 6.382087 TCACTAGGGACATATTGTGGTCTAT 58.618 40.000 0.00 0.00 34.49 1.98
2490 2616 5.773091 TCACTAGGGACATATTGTGGTCTA 58.227 41.667 0.00 0.00 34.49 2.59
2491 2617 4.620723 TCACTAGGGACATATTGTGGTCT 58.379 43.478 0.00 0.00 34.49 3.85
2492 2618 4.406003 ACTCACTAGGGACATATTGTGGTC 59.594 45.833 0.00 0.00 0.00 4.02
2493 2619 4.362677 ACTCACTAGGGACATATTGTGGT 58.637 43.478 0.00 0.00 0.00 4.16
2494 2620 4.651503 AGACTCACTAGGGACATATTGTGG 59.348 45.833 0.00 0.00 0.00 4.17
2495 2621 5.596361 AGAGACTCACTAGGGACATATTGTG 59.404 44.000 5.02 0.00 0.00 3.33
2496 2622 5.772004 AGAGACTCACTAGGGACATATTGT 58.228 41.667 5.02 0.00 0.00 2.71
2497 2623 7.001674 ACTAGAGACTCACTAGGGACATATTG 58.998 42.308 13.28 0.00 40.86 1.90
2498 2624 7.156694 ACTAGAGACTCACTAGGGACATATT 57.843 40.000 13.28 0.00 40.86 1.28
2499 2625 6.773583 ACTAGAGACTCACTAGGGACATAT 57.226 41.667 13.28 0.00 40.86 1.78
2500 2626 6.158169 TCAACTAGAGACTCACTAGGGACATA 59.842 42.308 13.28 0.00 40.86 2.29
2501 2627 5.044772 TCAACTAGAGACTCACTAGGGACAT 60.045 44.000 13.28 0.00 40.86 3.06
2502 2628 4.288887 TCAACTAGAGACTCACTAGGGACA 59.711 45.833 13.28 0.00 40.86 4.02
2503 2629 4.637091 GTCAACTAGAGACTCACTAGGGAC 59.363 50.000 13.28 14.42 40.86 4.46
2504 2630 4.536888 AGTCAACTAGAGACTCACTAGGGA 59.463 45.833 14.14 0.00 42.40 4.20
2505 2631 4.850680 AGTCAACTAGAGACTCACTAGGG 58.149 47.826 14.14 6.74 42.40 3.53
2506 2632 5.526111 GCTAGTCAACTAGAGACTCACTAGG 59.474 48.000 20.43 10.06 46.80 3.02
2507 2633 6.346096 AGCTAGTCAACTAGAGACTCACTAG 58.654 44.000 20.43 15.92 46.80 2.57
2508 2634 6.302535 AGCTAGTCAACTAGAGACTCACTA 57.697 41.667 20.43 1.96 46.80 2.74
2509 2635 5.174037 AGCTAGTCAACTAGAGACTCACT 57.826 43.478 20.43 16.67 46.80 3.41
2510 2636 4.033587 CGAGCTAGTCAACTAGAGACTCAC 59.966 50.000 20.43 15.25 46.80 3.51
2511 2637 4.185394 CGAGCTAGTCAACTAGAGACTCA 58.815 47.826 20.43 10.34 46.80 3.41
2512 2638 4.186159 ACGAGCTAGTCAACTAGAGACTC 58.814 47.826 20.43 14.26 46.80 3.36
2513 2639 4.210724 ACGAGCTAGTCAACTAGAGACT 57.789 45.455 19.03 20.58 46.80 3.24
2514 2640 4.154556 ACAACGAGCTAGTCAACTAGAGAC 59.845 45.833 19.03 4.30 46.80 3.36
2515 2641 4.154375 CACAACGAGCTAGTCAACTAGAGA 59.846 45.833 19.03 0.00 46.80 3.10
2516 2642 4.154375 TCACAACGAGCTAGTCAACTAGAG 59.846 45.833 19.03 11.89 46.80 2.43
2517 2643 4.070009 TCACAACGAGCTAGTCAACTAGA 58.930 43.478 19.03 0.00 46.80 2.43
2518 2644 4.421033 TCACAACGAGCTAGTCAACTAG 57.579 45.455 11.99 11.99 46.63 2.57
2519 2645 4.457949 TGATCACAACGAGCTAGTCAACTA 59.542 41.667 0.00 0.00 0.00 2.24
2520 2646 3.255888 TGATCACAACGAGCTAGTCAACT 59.744 43.478 0.00 0.00 0.00 3.16
2521 2647 3.575630 TGATCACAACGAGCTAGTCAAC 58.424 45.455 0.00 0.00 0.00 3.18
2522 2648 3.934457 TGATCACAACGAGCTAGTCAA 57.066 42.857 0.00 0.00 0.00 3.18
2523 2649 3.575630 GTTGATCACAACGAGCTAGTCA 58.424 45.455 0.00 0.00 45.06 3.41
2534 2660 6.053632 ACCATGACTATCTGTTGATCACAA 57.946 37.500 0.00 0.00 33.87 3.33
2535 2661 5.682234 ACCATGACTATCTGTTGATCACA 57.318 39.130 0.00 0.00 34.32 3.58
2536 2662 6.037610 GGAAACCATGACTATCTGTTGATCAC 59.962 42.308 0.00 0.00 34.32 3.06
2537 2663 6.070021 AGGAAACCATGACTATCTGTTGATCA 60.070 38.462 0.00 0.00 34.32 2.92
2538 2664 6.259608 CAGGAAACCATGACTATCTGTTGATC 59.740 42.308 0.00 0.00 34.32 2.92
2539 2665 6.118170 CAGGAAACCATGACTATCTGTTGAT 58.882 40.000 0.00 0.00 36.74 2.57
2540 2666 5.491070 CAGGAAACCATGACTATCTGTTGA 58.509 41.667 0.00 0.00 0.00 3.18
2541 2667 4.637534 CCAGGAAACCATGACTATCTGTTG 59.362 45.833 0.00 0.00 0.00 3.33
2542 2668 4.848357 CCAGGAAACCATGACTATCTGTT 58.152 43.478 0.00 0.00 0.00 3.16
2543 2669 3.370953 GCCAGGAAACCATGACTATCTGT 60.371 47.826 0.00 0.00 0.00 3.41
2544 2670 3.118112 AGCCAGGAAACCATGACTATCTG 60.118 47.826 0.00 0.00 0.00 2.90
2545 2671 3.118531 AGCCAGGAAACCATGACTATCT 58.881 45.455 0.00 0.00 0.00 1.98
2546 2672 3.567478 AGCCAGGAAACCATGACTATC 57.433 47.619 0.00 0.00 0.00 2.08
2547 2673 4.202503 CCATAGCCAGGAAACCATGACTAT 60.203 45.833 0.00 0.00 0.00 2.12
2548 2674 3.136443 CCATAGCCAGGAAACCATGACTA 59.864 47.826 0.00 0.00 0.00 2.59
2549 2675 2.092212 CCATAGCCAGGAAACCATGACT 60.092 50.000 0.00 0.00 0.00 3.41
2550 2676 2.092429 TCCATAGCCAGGAAACCATGAC 60.092 50.000 0.00 0.00 30.71 3.06
2551 2677 2.092429 GTCCATAGCCAGGAAACCATGA 60.092 50.000 0.00 0.00 36.80 3.07
2552 2678 2.301346 GTCCATAGCCAGGAAACCATG 58.699 52.381 0.00 0.00 36.80 3.66
2553 2679 1.922447 TGTCCATAGCCAGGAAACCAT 59.078 47.619 0.00 0.00 36.80 3.55
2554 2680 1.367346 TGTCCATAGCCAGGAAACCA 58.633 50.000 0.00 0.00 36.80 3.67
2555 2681 2.689983 CAATGTCCATAGCCAGGAAACC 59.310 50.000 0.00 0.00 36.80 3.27
2556 2682 2.689983 CCAATGTCCATAGCCAGGAAAC 59.310 50.000 0.00 0.00 36.80 2.78
2557 2683 2.580322 TCCAATGTCCATAGCCAGGAAA 59.420 45.455 0.00 0.00 36.80 3.13
2558 2684 2.204463 TCCAATGTCCATAGCCAGGAA 58.796 47.619 0.00 0.00 36.80 3.36
2559 2685 1.891933 TCCAATGTCCATAGCCAGGA 58.108 50.000 0.00 0.00 0.00 3.86
2560 2686 2.158564 ACATCCAATGTCCATAGCCAGG 60.159 50.000 0.00 0.00 39.92 4.45
2561 2687 3.219176 ACATCCAATGTCCATAGCCAG 57.781 47.619 0.00 0.00 39.92 4.85


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.